uci-cbcl/genomix — pull request #40 by anbangx (2013-10-25 00:44:33+00:00)
Title: Anbangx/debug bubble merge

A couple of changes in this feature branch:

1. Add output graphviz option to driver. Now you just now to specify -localGraphOutput and you can get the local graphviz output.

2. Add some optional log to bubblemerge to log the major vertex

3. For hg19 and dsm data, BubbleMerge pattern doesn't change the graph, though it doesn't cause any error. In order to double check that the graph really doesn't exist bubble, I need to extract subgraph by input major vertex(defined in bubble merge, remember?) as startSeed(you can start from this 'startSeed' and hop any times(set from parameter)). For bubble merge, we can only set the numOfHops as 2. It's good enough to check if it exists valid bubble. Now you just need to run "./extractSubgraph.sh hdfsInput localGraphOutput startSeed numOfHops" under the genomix/driver and then you can get the subgraph in the localGraphOutput directory you specify.

4. Fix a small bug in bubble merge.

@JavierJia @jakebiesinger @Nan-Zhang Please have a look at them. Thank you so much.